The boy, who was not identified, faces a first-degree murder charge in connection with the fatal Englewood shooting.
He was arrested in the 100-block of East Chicago Avenue Wednesday after being identified as one of the suspects involved in the incident, Chicago police said.
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About 4:20 p.m. Aug. 19, 23-year-old Keewaan Crayton was on a Red Line train traveling in the 200-block of West Garfield Boulevard when three people approached him and one of them fired shots, Chicago police said at the time.
Crayton was struck in the arm and taken to the University of Chicago Medical Center, where he died, police said.
Area One detectives are investigating.
Sun-Times Media contributed to this report.